Zinc in PDB 8hxw: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
Protein crystallography data
The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid, PDB code: 8hxw
was solved by
Y.-H.Yan,
K.-R.Zhu,
G.-B.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.81 /
2.39
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.71,
90.221,
125.904,
90,
90,
90
|
R / Rfree (%)
|
16.3 /
25
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
(pdb code 8hxw). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid, PDB code: 8hxw:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8hxw
Go back to
Zinc Binding Sites List in 8hxw
Zinc binding site 1 out
of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:44.0
occ:1.00
|
O
|
A:HOH427
|
1.6
|
53.0
|
1.0
|
NE2
|
A:HIS179
|
1.9
|
44.5
|
1.0
|
ND1
|
A:HIS116
|
2.0
|
45.2
|
1.0
|
NE2
|
A:HIS114
|
2.1
|
42.0
|
1.0
|
CD2
|
A:HIS179
|
2.8
|
39.1
|
1.0
|
CE1
|
A:HIS116
|
2.9
|
45.5
|
1.0
|
CE1
|
A:HIS114
|
3.0
|
38.3
|
1.0
|
CE1
|
A:HIS179
|
3.0
|
41.9
|
1.0
|
CG
|
A:HIS116
|
3.0
|
47.3
|
1.0
|
CD2
|
A:HIS114
|
3.1
|
41.8
|
1.0
|
CB
|
A:HIS116
|
3.4
|
38.1
|
1.0
|
ZN
|
A:ZN302
|
3.6
|
57.1
|
1.0
|
OD1
|
A:ASP118
|
3.9
|
37.3
|
1.0
|
CG
|
A:HIS179
|
4.0
|
43.5
|
1.0
|
ND1
|
A:HIS179
|
4.0
|
38.0
|
1.0
|
ND1
|
A:HIS114
|
4.1
|
34.7
|
1.0
|
NE2
|
A:HIS116
|
4.1
|
45.0
|
1.0
|
SG
|
A:CYS198
|
4.1
|
40.7
|
1.0
|
CD2
|
A:HIS116
|
4.1
|
42.9
|
1.0
|
CG
|
A:HIS114
|
4.1
|
39.5
|
1.0
|
CB
|
A:CYS198
|
4.2
|
42.7
|
1.0
|
O07
|
A:5ZR303
|
4.3
|
53.7
|
1.0
|
OD2
|
A:ASP118
|
4.4
|
46.3
|
1.0
|
CG
|
A:ASP118
|
4.6
|
43.5
|
1.0
|
CA
|
A:HIS116
|
4.8
|
41.6
|
1.0
|
N03
|
A:5ZR303
|
4.9
|
48.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8hxw
Go back to
Zinc Binding Sites List in 8hxw
Zinc binding site 2 out
of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:57.1
occ:1.00
|
OD2
|
A:ASP118
|
2.1
|
46.3
|
1.0
|
NE2
|
A:HIS240
|
2.3
|
53.0
|
1.0
|
O07
|
A:5ZR303
|
2.3
|
53.7
|
1.0
|
N03
|
A:5ZR303
|
2.3
|
48.3
|
1.0
|
SG
|
A:CYS198
|
2.5
|
40.7
|
1.0
|
O
|
A:HOH427
|
2.6
|
53.0
|
1.0
|
CE1
|
A:HIS240
|
3.0
|
48.0
|
1.0
|
C04
|
A:5ZR303
|
3.1
|
60.6
|
1.0
|
C05
|
A:5ZR303
|
3.1
|
55.0
|
1.0
|
CG
|
A:ASP118
|
3.2
|
43.5
|
1.0
|
C02
|
A:5ZR303
|
3.4
|
46.0
|
1.0
|
CD2
|
A:HIS240
|
3.4
|
52.6
|
1.0
|
OD1
|
A:ASP118
|
3.6
|
37.3
|
1.0
|
ZN
|
A:ZN301
|
3.6
|
44.0
|
1.0
|
CB
|
A:CYS198
|
3.7
|
42.7
|
1.0
|
N01
|
A:5ZR303
|
3.8
|
44.6
|
1.0
|
NH2
|
A:ARG119
|
4.0
|
41.4
|
1.0
|
ND1
|
A:HIS240
|
4.2
|
43.1
|
1.0
|
NE2
|
A:HIS179
|
4.3
|
44.5
|
1.0
|
O06
|
A:5ZR303
|
4.3
|
54.5
|
1.0
|
CE1
|
A:HIS179
|
4.3
|
41.9
|
1.0
|
C08
|
A:5ZR303
|
4.4
|
55.5
|
1.0
|
NE
|
A:ARG119
|
4.4
|
39.4
|
1.0
|
CB
|
A:ASP118
|
4.4
|
39.8
|
1.0
|
CG
|
A:HIS240
|
4.4
|
46.2
|
1.0
|
CE1
|
A:HIS114
|
4.6
|
38.3
|
1.0
|
NE2
|
A:HIS114
|
4.7
|
42.0
|
1.0
|
CZ
|
A:ARG119
|
4.7
|
40.3
|
1.0
|
S16
|
A:5ZR303
|
4.7
|
61.4
|
1.0
|
CA
|
A:CYS198
|
4.9
|
44.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8hxw
Go back to
Zinc Binding Sites List in 8hxw
Zinc binding site 3 out
of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:39.2
occ:1.00
|
ND1
|
B:HIS116
|
1.9
|
38.5
|
1.0
|
NE2
|
B:HIS179
|
2.0
|
43.6
|
1.0
|
NE2
|
B:HIS114
|
2.1
|
41.4
|
1.0
|
O
|
B:HOH406
|
2.4
|
45.6
|
1.0
|
CE1
|
B:HIS116
|
2.8
|
37.6
|
1.0
|
CE1
|
B:HIS179
|
2.9
|
40.2
|
1.0
|
CD2
|
B:HIS179
|
3.0
|
41.1
|
1.0
|
CE1
|
B:HIS114
|
3.0
|
42.3
|
1.0
|
CG
|
B:HIS116
|
3.0
|
37.9
|
1.0
|
CD2
|
B:HIS114
|
3.2
|
41.0
|
1.0
|
CB
|
B:HIS116
|
3.5
|
39.2
|
1.0
|
ZN
|
B:ZN302
|
3.6
|
52.7
|
1.0
|
NE2
|
B:HIS116
|
4.0
|
35.7
|
1.0
|
OD1
|
B:ASP118
|
4.0
|
31.4
|
1.0
|
ND1
|
B:HIS179
|
4.0
|
37.2
|
1.0
|
CG
|
B:HIS179
|
4.1
|
41.4
|
1.0
|
CD2
|
B:HIS116
|
4.1
|
34.5
|
1.0
|
SG
|
B:CYS198
|
4.1
|
44.9
|
1.0
|
ND1
|
B:HIS114
|
4.2
|
39.5
|
1.0
|
CB
|
B:CYS198
|
4.3
|
38.4
|
1.0
|
CG
|
B:HIS114
|
4.3
|
41.9
|
1.0
|
O07
|
B:5ZR303
|
4.4
|
52.9
|
1.0
|
OD2
|
B:ASP118
|
4.7
|
38.4
|
1.0
|
CG
|
B:ASP118
|
4.8
|
35.6
|
1.0
|
CA
|
B:HIS116
|
4.9
|
38.6
|
1.0
|
N03
|
B:5ZR303
|
4.9
|
41.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8hxw
Go back to
Zinc Binding Sites List in 8hxw
Zinc binding site 4 out
of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/hx/8hxw-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:52.7
occ:1.00
|
O
|
B:HOH406
|
1.7
|
45.6
|
1.0
|
NE2
|
B:HIS240
|
2.2
|
43.6
|
1.0
|
OD2
|
B:ASP118
|
2.2
|
38.4
|
1.0
|
O07
|
B:5ZR303
|
2.4
|
52.9
|
1.0
|
SG
|
B:CYS198
|
2.5
|
44.9
|
1.0
|
N03
|
B:5ZR303
|
2.6
|
41.9
|
1.0
|
CE1
|
B:HIS240
|
2.9
|
41.0
|
1.0
|
CG
|
B:ASP118
|
3.2
|
35.6
|
1.0
|
C05
|
B:5ZR303
|
3.3
|
47.0
|
1.0
|
C04
|
B:5ZR303
|
3.4
|
52.7
|
1.0
|
CD2
|
B:HIS240
|
3.4
|
42.5
|
1.0
|
OD1
|
B:ASP118
|
3.5
|
31.4
|
1.0
|
C02
|
B:5ZR303
|
3.5
|
40.3
|
1.0
|
ZN
|
B:ZN301
|
3.6
|
39.2
|
1.0
|
CB
|
B:CYS198
|
3.7
|
38.4
|
1.0
|
N01
|
B:5ZR303
|
3.8
|
36.6
|
1.0
|
NH2
|
B:ARG119
|
4.0
|
37.9
|
1.0
|
ND1
|
B:HIS240
|
4.1
|
40.1
|
1.0
|
NE2
|
B:HIS179
|
4.4
|
43.6
|
1.0
|
CG
|
B:HIS240
|
4.4
|
42.0
|
1.0
|
CE1
|
B:HIS179
|
4.4
|
40.2
|
1.0
|
O06
|
B:5ZR303
|
4.4
|
55.7
|
1.0
|
NE
|
B:ARG119
|
4.5
|
29.1
|
1.0
|
CB
|
B:ASP118
|
4.6
|
32.9
|
1.0
|
CE1
|
B:HIS114
|
4.6
|
42.3
|
1.0
|
C08
|
B:5ZR303
|
4.7
|
57.4
|
1.0
|
CZ
|
B:ARG119
|
4.7
|
33.1
|
1.0
|
NE2
|
B:HIS114
|
4.7
|
41.4
|
1.0
|
CA
|
B:CYS198
|
4.9
|
48.2
|
1.0
|
S16
|
B:5ZR303
|
5.0
|
52.3
|
1.0
|
|
Reference:
Y.H.Yan,
T.T.Zhang,
R.Li,
S.Y.Wang,
L.L.Wei,
X.Y.Wang,
K.R.Zhu,
S.R.Li,
G.Q.Liang,
Z.B.Yang,
L.L.Yang,
S.Qin,
G.B.Li.
Discovery of 2-Aminothiazole-4-Carboxylic Acids As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors By Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. V. 66 13746 2023.
ISSN: ISSN 0022-2623
PubMed: 37791640
DOI: 10.1021/ACS.JMEDCHEM.3C01189
Page generated: Thu Dec 28 13:14:25 2023
|